PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Alterations in Secondary Lipids Are Associated with Neuroinflammation in the Brain of Neu1-Deficient Mice(Springer, 2026) Ada, Ebru; Seyrantepe, VolkanNeu1 (lysosomal sialidase 1) is essential for removing sialic acid from oligosaccharides and glycoconjugates. Neu1 deficiency impairs lysosomal digestion, leading to sialidosis and sialoglycoprotein accumulation. It also increases lipids, including gangliosides GM3, GD3, GM4, and LM1, in the kidney, liver, and spleen. Neu1-/- mice display symptoms resembling Type II sialidosis, including enlarged spleen and liver, kidney issues, neurological problems, spinal defects, and oligosaccharide buildup. The study examined secondary lipid alterations and inflammation in the cortex and cerebellum of these mice. Lipidomic, molecular, and immunohistochemical analyses of tissues from 2 and 5 M Neu1-/- mice revealed reduced levels of lipids, including PC, PE, PS, and CL, along with increased pro-inflammatory cytokines and loss of oligodendrocytes and neurons. Signs of astrogliosis and microgliosis emerged in specific brain regions. These results indicate that reduced levels of glycerophospholipids could serve as an indicator of inflammation in sialidosis mice. Future research should investigate therapies targeting these lipid changes, as modulating glycerophospholipids might slow disease progression in sialidosis patients.Article Mass Spectrometric Profiling Reveals Alterations in N-Glycans and O-Glycans in Tay-Sachs Disease Under Autophagy-Induced Conditions(Springer, 2025) Can, Melike; Basirli, Hande; Jin, Chunsheng; Karlsson, Niclas G.; Bojar, Daniel; Seyrantepe, VolkanTay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the alpha-subunit of the enzyme beta-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.Article Citation - WoS: 7Citation - Scopus: 9A Holistic Overview of the Applications of Grace-Observed Terrestrial Water Storage in Hydrology and Climate Science(Springer, 2025) Khorrami, Behnam; Gunduz, OrhanTerrestrial Water Storage (TWS) represents a vital element of the hydrological cycle, with its fluctuations significantly impacting the climate of the Earth and its ecological balance. Since its launch in 2002, the Gravity Recovery and Climate Experiment (GRACE) satellite mission has revolutionized the ability to observe and analyze large-scale mass changes within Earth's system components. This paper offers a comprehensive and current overview of GRACE satellite gravimetry, highlighting its relevance to hydrological and climate-related studies. It outlines the fundamental measurement principles of the GRACE mission, provides an in-depth explanation of GRACE data products (including spherical harmonic and mascon solutions), examines emerging trends in GRACE-based research, and reviews key applications in hydrology and climate science. Additionally, it addresses the major challenges in utilizing GRACE data and explores promising avenues for future research and applications.Article Citation - WoS: 1Citation - Scopus: 1Imbalance in Redox Homeostasis Is Associated With Neurodegeneration in the Murine Model of Tay-Sachs Disease(Springer, 2025) Basirli, Hande; Ates, Nurselin; Seyrantepe, VolkanBackgroundTay-Sachs disease is a neurodegenerative disorder characterized by a build-up of GM2 ganglioside in the brain, which results in progressive central nervous system dysfunction. Our group recently generated Hexa-/-Neu3-/- mice, a murine model with neuropathological abnormalities similar to the infantile form of Tay-Sachs disease. Previously, we reported progressive neurodegeneration with neuronal loss in the brain sections of Hexa-/-Neu3-/- mice. However, the relationship between the severity of neurodegeneration and the imbalance in redox homeostasis was not yet clarified in Hexa-/-Neu3-/- mice. Here, we evaluated whether neurodegeneration is associated with oxidative stress in the tissues and cells of Hexa-/-Neu3-/- mice and neuroglia cells from Tay-Sachs patients.Methods and resultsCell death and oxidative stress-related markers were evaluated in four brain regions and fibroblasts of 5-month-old WT, Hexa-/-, Neu3-/-, and Hexa-/-Neu3-/- mice and human neuroglia cells using Western blot, RT-PCR, and immunohistochemistry analyses. We further analyzed oxidative stress levels in the samples using flow cytometry analyses. We discovered neuronal death, alterations in intracellular ROS levels, and damaging effects of oxidative stress, especially in the cerebellum and fibroblasts of Hexa-/-Neu3-/- mice.ConclusionsOur results showed that alteration in redox homeostasis might be related to neurodegeneration in the murine model of Tay-Sachs Disease. These findings suggest that targeting the altered redox balance and increased oxidative stress might be a rational therapeutic approach for alleviating neurodegeneration and treating Tay-Sachs disease.Correction 3D modelling of surface spreading and underground dam groundwater recharge: Egri creek subbasin, Turkey(Springer, 2023) Şahin, Yavuz; Tayfur, GökmenArticle Citation - WoS: 21Citation - Scopus: 21Remote Sensing-Based Monitoring and Evaluation of the Basin-Wise Dynamics of Terrestrial Water and Groundwater Storage Fluctuations(Springer, 2023) Khorrami, Behnam; Gündüz, OrhanThe recent dynamics of terrestrial water storage (TWS) and groundwater storage (GWS) fluctuations were investigated based on the Gravity Recovery And Climate Experiment (GRACE) observations over 25 basins of Türkiye. Coarse-resolution GRACE estimates were downscaled based on the Random Forest algorithm. The impacts of precipitation (P) and evapotranspiration (ET) on the variations of water storage were also assessed. The findings demonstrated good performance for the RF model in simulating finer resolution estimates of TWS. The results indicated a diminishing trend of TWS and its hydrologic components over all the basins from 2003 to 2020. The Doğu Akdeniz Basin with the annually decreasing TWS and GWS of 1.15cm/yr and 1.10cm/yr was the most critical basin of Türkiye. The least storage loss was observed in the Batı Karadeniz Basin with the annual TWS and GWS loss of 0.38cm/yr and 0.45cm/yr , respectively. Based on the results, Türkiye has lost, on average, an estimated 5.16km3/yr and 4.09km3/yr of its TWS and GWS, respectively, which are equivalent to the total storage loss of 92.88km3 and 73.62km3 of TWS and GWS during the last 18 years. The results also indicated that P and ET interact differently with the variations of TWS and GWS. The net water flux was revealed to be partially correlated with the total water storage fluctuations, suggesting the governing role of other deriving forces particularly the anthropogenic factors in the spatiotemporal variations of Türkiye’s water storage; therefore, a sector-specific analysis of the water storage variations is crucial for the country, particularly by concentrating more on the dynamics of GWS. Graphical Abstract: [Figure not available: see fulltext.]. © 2023, The Author(s), under exclusive licence to Springer Nature Switzerland AG.Article Citation - WoS: 4Citation - Scopus: 53d Modelling of Surface Spreading and Underground Dam Groundwater Recharge: Egri Creek Subbasin, Turkey(Springer, 2023) Şahin, Yavuz; Tayfur, GökmenThis study investigated surface spreading and underground dam recharge methods to replenish groundwater in Turkey's Egri Creek Sub-basin of the Kucuk Menderes River Basin. A three-dimensional numerical model was employed for this purpose. Field and lab data are provided to the model for realistic simulations. Pumping test results were used to determine the aquifer parameters. The laboratory works involved sieve analysis, permeability tests, and porosity and water content prediction. The numerical model's boundary conditions were determined from the geological and hydrogeological characteristics of the study area. Initial conditions were expressed regarding water content and pressure head in the vadose zone. The numerical model was satisfactorily validated by simulating water levels in three different pumping wells in the study area. Seven different scenarios, each having a different pool size, were investigated for the surface spreading recharge method. The results showed that a pool size of 30 x 30 m with a 6-m depth basin was the most optimal choice, raising the groundwater level to about 29.3 m. On the other hand, it was found that an underground dam could raise the levels by an average of 9.5 m, which might not be significant to warrant the construction.Article Assessment of Undergraduate Health Students' Perception and Satisfaction on Training and Participation in Community Health Outreach(Springer, 2023) Adegbore, Abidemi Kafayat; Adedokun, Amudatu Ambali; Adegoke, Juliet Ifeoluwa; Lawal, Maruf Ayobami; Oke, MuseAimThe need to improve training of health professionals has increased in recent years due to increasing frequencies of public health events. Consequently, a descriptive cross-sectional survey was carried out to determine the level of satisfaction and knowledge acquired by undergraduate students in the health sciences during a community health outreach program.Subject and methodsStudents were invited to complete an online-administered questionnaire (consisting of both open- and closed-ended questions) to assess their perceptions and experiences on the community health outreach program. Additionally, the survey was carried out to assess the quality of training provided and obtain suggestions for further improvements. Responses were collected and analysed using Microsoft Excel.ResultsMost respondents (>83%) reported satisfaction with the community diagnosis and community intervention briefing and training sessions. All respondents reported familiarity with standard community health outreach instruments and were capable of identifying environmental health risk factors that may contribute to the spread of communicable diseases. Interestingly, respondents reported greater appreciation of health challenges faced by rural communities. However, respondents expressed dissatisfaction with the duration of the outreach program (24%) and funding (15%).ConclusionAlthough respondents reported overall satisfaction with the organization and execution of the health outreach program, certain aspects of the program were deemed unsatisfactory. Despite the shortcomings, we believe that our student-centred learning strategy is readily adaptable for training future healthcare professionals and improving health literacy of rural communities, particularly in sub-Saharan Africa.Article Citation - WoS: 6Citation - Scopus: 6Diagnosis of Ruminant Viral Diseases With Loop-Mediated Isothermal Amplification(Springer, 2023) Ayaz Kök, Sanem; Üstün, Selcen; Taşkent, HümeyraInfectious diseases in livestock industry are major problems for animal health, food safety, and the economy. Zoonotic diseases from farm animals are significant threat to human population as well. These are notifiable diseases listed by the World Organization for Animal Health (OIE). Rapid diagnostic methods can help keep infectious diseases under control in herds. Loop-mediated isothermal amplification (LAMP) is a simple and rapid nucleic acid amplification method that is studied widely for detection of many infectious diseases in the field. LAMP allows biosensing of target DNA or RNA under isothermal conditions with high specificity in a short period of time. An untrained user can analyze results based on color change or turbidity. Here we review LAMP assays to diagnose OIE notifiable ruminant viral diseases in literature highlighting properties of LAMP method considering what is expected from an efficient, field usable diagnostic test.Article Citation - WoS: 3Citation - Scopus: 3Gras-Di Snp-Based Molecular Characterization and Fingerprinting of a Turkish Corylus Avellana Core Set Provide Insights Into the Cultivation and Breeding of Hazelnut in Turkey(Springer, 2023) Yanar, Ertuğrul Gazi; Doğanlar, Sami; Frary, AnneHazelnut (Corylus avellana L.) is an economically and socially important product for Turkey, the country that leads global production of this crop. The preservation of Turkish hazelnut genetic diversity and informed breeding of new cultivars are crucial for maintaining quality and crop yield stability. In this study, genotyping by random amplicon sequencing (GRAS-Di) was used to identify single-nucleotide polymorphisms (SNPs) in a panel of 96 individuals representing the Turkish national hazelnut collection. The resulting 7609 high-quality SNPs were physically mapped to the Tombul cultivar reference genome and used for population structure and diversity analyses. These analyses revealed that cultivars are not less diverse than wild accessions and that 44% of the panel had admixed ancestry. The results also indicated that recently released Turkish cultivars are highly similar to each other, suggesting that diversity analysis is an important tool that should be employed to prevent future genetic bottlenecks in this crop. A minimal marker algorithm was used to select a set of seven SNP markers that were capable of differentiating the panel accessions. These fingerprinting markers should be useful for the propagation of true-to-type elite cultivars that can be used to renew Turkey's aging hazelnut orchards.